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Publications Prior to 2010

Klattenhoff C, Xi H, Li C, Lee S, Xu J, Khurana JS, Zhang F, Schultz N, Koppetsch BS, Nowosielska A, Seitz H, Zamore PD+, Weng Z+, Theurkauf WE(2009) 
The Drosophila HP1 homolog Rhino is required for transposon silencing and piRNA production by dual-strand clusters. 
Cell, 18;138(6):1137-49. (PMCID: PMC2770713) 
+Co-corresponding authors.

Yu L, Coelho JE, Zhang X, Fu Y, Tillman A, Karaoz U, Fredholm BBWeng Z, Chen JF. (2009) 
Uncovering multiple molecular targets for caffeine using a drug target validation strategy combining A 2A receptor knockout mice with microarray profiling. 
Physiol Genomics13;37(3):199-210. (PMCID: PMC2685498).

Li C, Vagin VV, Lee S, Xu J, Ma S, Xi H, Seitz H, Horwich M, Syrzycka M, Honda, B., Kittler E, Zapp M, Klattenhoff C, Schulz N, Theurkauf W, Weng Z +, Zamore PD + (2009) 
Collapse of Germline piRNAs in the Absence of Argonaute3 Reveals Somatic piRNAs in Flies. 
Cell1;137(3):509-21. (PMCID: PMC2768572) 
+Co-corresponding authors.

Haidar JN*, Pierce B*, Yu Y, Tong W, Li M, and Weng, Z. (2009) 
Structure-Based Design of a T-Cell Receptor Leads to Nearly 100-Fold Improvement in Binding Affinity for pepMHC. 
Proteins: Structure, Function, and Bioinformatics, 74(4):948-960. (PMCID: PMC2696811) 
*Joint first authors.

Lee S, Kasif S, Weng Z+, Cantor CR+. (2008) 
Quantitative analysis of single nucleotide polymorphisms within copy number variation.  
PLoS ONE 3(12):e3906 (PMCID: PMC2600609) 
+Co-corresponding authors.

Hwang H, Pierce B, Mintseris J, Janin J, and Weng Z. (2008)
Protein-protein docking benchmark version 3.0. 
Proteins: Structure, Function, and Bioinformatics, 73(3):705-709. (PMCID: PMC2726780).

Fu Y, Sinha M, Peterson CL, and Weng Z. (2008) 
The Insulator binding protein CTCF positions 20 nucleosomes around its binding sites across the human genome.  
PLoS Genet., July; 4(7): e1000138. (PMCID: PMC2453330).

Ghildiya M*, Seitz H*, Horwich M D, Li C, Du T, Lee S, Xu J, Kittler E L, Zapp ML, Weng Z, Zamore PD. (2008) 
Endogenous siRNAs Derived from Transposons and mRNAs in Drosophila Somatic Cells. 
Science, May 23;320(5879):1077-81. (PMCID: PMC2953241)
*Joint first authors.

Pierce B., Weng Z. (2008) 
A combination of rescoring and refinement significantly improves protein docking performance.
Proteins: Structure, Function, and Bioinformatics, 72(1):270-279. (PMCID: PMC2696687).

Zhang X*, Guo C*, Chen Y*, Shulha HP, Schnetz MP, LaFramboise T, Bartels CF, Markowitz S, Weng Z, Scacheri PC, Wang Z. (2008) 
Epitope tagging of endogenous proteins for genome-wide ChIP-chip studies.
Nat Methods. 5(2):163-5. (PMCID: PMC2435063)
*Joint first authors.

Johnson DS*, Li W*, Shulha HP, Fu Y, Weng Z, Struhl K, Myers RM, Lieb JD, Liu XS. (2008)
Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets. 
Genome Research, Mar;18(3): 393-403. (PMCID: PMC2259103)
*Joint first authors.

Weng Z, Guigó R (2008) 
In silico meets in vivo. 
Genome Biol. 2008; 9(2):302 (PMCID: PMC237416).

Boyle AP, Davis S, Shulha HP, Meltzer P, Margulies EH, Weng Z., Furey TS+, Crawford GE+. (2008) 
High-resolution mapping and characterization of open chromatin across the genome. 
Cell Jan 25;132(2):311-22. (PMCID: PMC2669738)

Wiehe K, Peterson MW, Pierce B, Mintseris J, Weng Z. (2007) 
Protein-protein docking: overview and performance analysis.
Methods Mol Biol 413, 283-314.

Wiehe K, Pierce B, Tong W, Hwang H, Mintseris J, Weng Z. (2007) 
The Performance of ZDOCK and ZRANK in Rounds 6-11 of CAPRI. 
Proteins: Structure, Function, and Bioinformatics, Dec 1;69(4), 719-725.

Xi H, Shulha HP, Lin JM, Vales TR, Fu Y, Bodine DM, McKay RDJ, Chenoweth JG, Tesar PJ, Furey TS, Ren B, Weng Z+, Crawford GE. + (2007) 
Identification and characterization of cell type-specific and ubiquitous chromatin regulatory structures in the human genome.
PLoS Genetics, Aug 17;3(8):e136.
+Co-corresponding authors.

Mintseris J, Pierce B, Wiehe K, Anderson R, Chen R,  Weng Z. (2007) 
Integrating Statistical Pair Potentials into Protein Complex Prediction. 
Proteins: Structure, Function, and Bioinformatics, Nov 15;69(3), 511-520.

Peckham HE, Thurman RE, Fu Y, Noble WS, Struhl K, Weng Z. (2007)
Nucleosome Positioning Signals in Genomic DNA. 
Genome Research, Aug;17(8):1170-7.

The ENCODE Project Consortium (Weng, Z. was a co-corresponding author and co-chair of the transcription regulation group) (2007) 
The ENCODE pilot project: Identification and analysis of functional elements in 1% of the human genome. 
Nature, Jun 14;447(7146):799-816.

Heintzman ND, Stuart RK, Hon G, Fu Y, Ching CW, Hawkins RD, Barrera LO, Calcar S V, Qu C, Ching KA, Wang W, Weng Z, Green RD, Crawford GE, Bing R. (2007) 
Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome.
Nature Genetics, Mar;39(3):311-318.

Trinklein ND*, Karaöz U*, Wu J*, Halees A*, Aldred SF, Collins PJ, Zheng D,  Zhang ZD, Gerstein M, Snyder M, Myers RM, Weng Z.  (2007) 
Integrated analysis of experimental datasets reveals many novel promters in 1% of the human genome. 
Genome Research, Jun;17(6):720-31.
*Joint first authors.

Xi H, Yu Y, Fu Y, Foley J, Halees A, Weng Z. (2007) 
Analysis of overrepresented motifs in human core promoters reveals dual regulatory roles of YY1.  
Genome Research, Jun;17(6):798-806.

Pierce B, Weng Z. (2007)
ZRANK: Reranking Protein Docking Predictions with an Optimized Energy Function. 
Proteins: Structure, Function, and Bioinformatics, Jun 1;67(4):1078-86.

Koch CM, Andrews RM, Flicek P, Dillon SC, Karaoz U, Clelland GK, Wilcox S, Beare DM, Fowler JC, Couttet P, James KD, Lefebvre GC, Bruce AW, Dovey OM, Ellis PD, Dhami P, Langford CF, Weng Z, Birney E, Carter NP, Vetrie D, Dunham, I. (2007) 
The landscape of activating histone modifications across 1% of the human genome.
Genome Research ENCODE Issue, Jun;17(6):691-707.

Lin JM, Collins PJ, Trinklein ND, Fu Y, Xi H, Myers RM, Weng Z. (2007) 
Transcription Factor Binding and Histone Modifications in Human Bidirectional Promoters. 
Genome Research ENCODE Issue, Jun;17(6):818-27.

Zhang ZD, Paccanaro A, Fu Y, Weissman S, Weng Z, Chang J, Snyder M, Gerstein M. (2007) 
Statistical analysis of the genomic distribution and correlation of regulatory elements in the ENCODE regions.. 
Genome Research ENCODE Issue, Jun;17(6):787-97.

Zeller KI, Zhao X, Lee CW, Chiu KP, Yao F, Yustein JT, Ooi HS, Orlov YL, Shahab A, Yong HC, Fu Y, Weng Z, Kuznetsov VA, Sung WK, Ruan Y, Dang CV, Wei CL. (2006) 
Global mapping of c-Myc binding sites and target gene networks in human B cells. 
PNAS, 103 (47):17834–17839.

Lin JM, Weng Z. (2006) 
Systematic Detection of Statistically Over-Represented DNA Motif Association Rules.
Genome Informatics, 17(1): 124-133.

Wei CL, Wu Q, Vega VB, Chiu KP, Ng P, Zhang T, Shahab A, Yong HC, Fu Y, Weng Z, Liu J, Zhao XD, Chew JL, Lee YL, Kuznetsov VA, Sung WK, Miller LD, Lim B, Liu ET, Yu Q, Ng HH, Ruan Y. (2006)

A global map of p53 transcription-factor binding sites in the human genome. 

Cell. 124(1):207-19.

Peckham HE, Weng Z. (2005) 
Identification of Conserved Structural Features at Sequentially Degenerate Locations in Transcription Factor Binding Sites.  
Genome Informatics 16(1): 49-58.

Fu Y, Weng Z. (2005) 
Improvement of TRANASFAC Matrices Using Multiple Local Alignment of Transcription Factor Binding Site Sequences.  
Genome Informatics 16(1): 68-72.

Yu L*, Haverty PM*, Mariani J, Wang Y, Shen H Y, Schwarzschild MA, Weng Z, Chen JF. (2005) 
Genetic and Pharmacological Inactivation of Adenosine A2A Receptor Reveals an Egr-2 Mediated Transcriptional Regulatory Network in the Mouse Striatum. 
Physiological Genomics 23(1), 89-102. *Joint first authors.

Peters B, Bui HH, Sidney J, Weng Z, Loffredo JT, Watkins DI, Mothe BR, Sette A. (2005) 
A computational resource for the prediction of peptide binding to Indian rhesus macaque MHC class I molecules. 
Vaccine 23(45), 5212-5224.

Leyfer D, Weng Z. (2005)
Genome-wide decoding of hierarchical modular structure of transcriptional regulation by cis-element and expression clustering.
Bioinformatics 21(Supplement 2), ii197-ii203.

Szustakowski JD, Kasif S, Weng Z. (2005) 
Less is more: towards an optimal universal description of protein folds 
Bioinformatics 21(Supplement 2), ii66-ii71.

Burden HE, Weng Z (2005) 
Identification of conserved structural features at sequentially degenerate locations in transcription factor binding sites. 
Genome Inform 2005; 16(1):49-58

Anderson RJ, Weng Z, Campbell RK, Jiang X. (2005) 
Main-chain conformational tendencies of amino acids.
Proteins: Structure Function, and Bioinformatics. 60(4), 679-689.

Mintseris J,  Weng Z. (2005) 
Structure, function, and evolution of transient and obligate protein-protein interactions.  
PNAS 102(31), 10930-10935.

Mintseris J, Wiehe K, Pierce B, Anderson R, Chen R, Janin J, Weng Z.  (2005) 
Protein-Protein Docking Benchmark 2.0: an Update. 
Proteins: Structure Function, and Bioinformatics. 60(2), 214-216.

Wiehe K, Pierce B, Mintseris J, Tong W, Anderson R, Chen R, Weng Z.  (2005) 
ZDOCK and RDOCK Performance in CAPRI Rounds 3, 4, and 5.
Proteins: Structure Function, and Bioinformatics 60(2), 207-213.

Pierce BG, Tong W, Weng Z. (2005) 
M-ZDOCK: A Grid-based Approach for Cn Symmetric Multimer Docking. 
Bioinformatics 21(8),1472-1476.

Haverty PM, Weng Z, Hansen U. (2005) 
Transcriptional Regulatory Networks Activated by PI3K and ERK Transduced Growth Signals in Human Glioblastoma Cells. 
J. Comput. Sci. & Tech. 20(4), 439-445.

Yanai I*, Yu Y*, Zhu X, Cantor C, Weng Z. (2005) 
An Avidin-like Domain that Does Not Bind Biotin Is Adopted for Oligomerization by the Extracellular Mosaic Protein Fibropellin. 
Protein Science, 14:417-423.
*Joint first authors.

Tompa M, Li N, Bailey TL, Church GM, De Moor B, Eskin E, Favorov AV, Frith MC, Fu Y, Kent WJ, Makeev VJ, Mironov AA, Noble WS, Pavesi G, Pesole G, Regnier M, Simonis N, Sinha S, Thijs G, van Helden J, Vandenbogaert M, Weng Z, Workman C, Ye C, Zhu Z. (2005)
Assessing computational tools for the discovery of transcription factor binding sites. 
Nat Biotechnol. 2005 Jan;23(1):137-44.

Zhu J, Weng Z. (2005) 
FAST: A Novel Protein Structure Alignment Algorithm. 
Proteins: Structure Function, and Bioinformatics. 58:618-627.

The ENCODE Project Consortium (2004) 
The ENCODE (ENCyclopedia Of DNA Elements) Project. 
Science, 306: 636-640.

Haverty PM, Hsiao L, Gullans SR, Hansen U, Weng Z. (2004) 
Limited Agreement among Three Global Gene Expression Methods Highlights the Requirement for Non-Global Validation.
Bioinformatics. 20:3431-3441.

Mintseris J, Weng Z (2004) 
Optimizing protein representations with information theory.
Genome Inform 2004; 15(1):160-9.

Hu Z, Fu Y, Halees AS, Kielbasa SM, Weng Z. (2004) 
SeqVISTA: a New Module of Integrated Computational Tools for Studying Transcriptional Regulation. 
Nucleic Acids Res., 32:W235-W241.

Leyfer D, Bond A, Tworog E, Perron D, Maska S, Brito A, Kamens J, Weng Z, Voss J. (2004)
cis- Element Clustering Correlates with Dose-Dependent Pro- and Anti- Signaling Effects of IL18. 
Genes and Immunity. June 10, 1-9.

Haverty PM, Frith MC, Weng Z. (2004) 
CARRIE Web Service: Automated Transcriptional Regulatory Network Inference and Interactive Analysis. 
Nucleic Acids Res. 32:W213-W216.

Fu Y, Frith MC, Haverty PM, Weng Z. (2004) 
MotifViz: an Analysis and Visualization Tool for Motif Discovery. 
Nucleic Acids Res. 32:W420-W423.

Halees AS, Weng Z. (2004). 
PromoSer: Improvements on Algorithm, Visualization and Accessibility. 
Nucleic Acids Res. 32:W191-W194.

Haverty PM, Weng Z. (2004). 
CisML, an XML-based Format for Sequence Motif Detection Software. 
Bioinformatics. 20:1815-1817.

Frith M, Fu Y, Yu L, Chen JF, Hansen U, Weng Z. (2004) 
Detection of Functional DNA Motifs via Statistical Overrepresentation.
Nucleic Acids Research. 32:1372-1381.

Frith M*, Halees A*, Hansen U, Weng Z.(2004) 
Site2genome: Locating Short DNA Sequences in Whole Genomes.  
Bioinformatics. 20:1468-1469. *Joint first authors.

Yu L, Frith M, Suzuki Y, Peterfreund RA, Gerean T, Sugano S, Schwarzschild MA, Weng Z, Fink JF, Chen JF. (2004)
Characterization of genomic organization of the adenosine A2A Receptor Gene by Molecular and Bioinformatics Analyses.  
Brain Research. 1000:156-171.

Haverty PM, Hansen U, Weng Z. (2004)
Computational Inference of Transcriptional Regulatory Networks from Expression Profiling and Transcription Factor Binding Site Identification. 
Nucleic Acids Research. 32:179-188.

Frith MC, Hansen U, Spouge JL, Weng Z. (2004) 
Finding Functional Sequence Elements by Multiple Local Alignment.  
Nucleic Acids Research. 32:189-200.

Li L*, Chen R*, Weng Z. (2003) 
RDOCK: Refinement of Rigid-body Protein-Protein Docking Predictions. 
Proteins. Structure, Function and Genetics. 53:693-707. *Joint first authors.

Weng Z (2003) 
Managing biological sequence and protein structure data.
OMICS 2003; 7(1):25-6.

Mintseris J, Weng Z. (2003)
Atomic contact vectors in protein-protein recognition. 
Proteins. Structure, Function and Genetics.  53:629-639.

Peters B, Tong W, Sidney J, Sette A, Weng Z. (2003) 
Examining the binding of peptide epitopes to class I MHC molecules: experimental noise and the independent binding assumption.  
Bioinformatics. 19:1765-1772.

Halees AS, Leyfer D, Weng Z. (2003) 
PromoSer: A large-scale mammalian promoter and transcription start site identification service. 
Nucleic Acids Research. 31:3554-3559.

Frith MC, Li MC,  Weng Z. (2003) 
Cluster-Buster:  Finding Dense Clusters of Motifs in DNA Sequences.
Nucleic Acids Research. 31:3666-3668.

Chen R, Tong W, Mintseris J, Li L, Weng Z. (2003) 
ZDOCK Predictions for the CAPRI Challenge.  
Proteins. Structure, Function and Genetics. 52:68-73.

Chen R, Li L,  Weng Z. (2003)  
ZDOCK: An Initial-stage Protein Docking Algorithm. 
Proteins. Structure, Function and Genetics. 52:80-87.

Chen R, Mintseris J, Janin J, Weng Z. (2003)  
A Protein-protein Docking Benchmark.
Proteins. Structure, Function and Genetics. 52:88-91.

Chen, R. Weng, Z. (2003)
A novel shape-complementarity scoring function for protein-protein docking. 
Proteins. Structure, Function and Genetics.  51: 397-408.  

Hu Z, Frith M, Niu T, Weng Z.  (2003)
SeqVISTA: a graphical tool for sequence feature visualization and comparison.
BMC Bioinformatics. 4:1. 

Kasif S*, Weng Z*, Derti A, Beigel R, DeLisi C. (2002) 
A computational framework for optimal masking in the synthesis of oligonucleotide microarrays. 
Nucleic Acid Research. 30(20): e106. *Joint first authors.  

Wong JY, Weng Z, Moll S, Kim S, Brown C. (2002) 
Identification and validation of a novel cell-recognition site (KNEED) on the 8th type III domain of fibronectin. 
Biomaterials. 23: 3865-3870. 

Frith M, Spouge J, Hansen U, Weng Z. (2002) 
Statistical significance of clusters of motifs represented by position specific scoring matrices in nucleotide sequences. 
Nucleic Acid Research. 30:3214-3224. 

Chen R, Weng Z. (2002)
Docking unbound proteins using shape complementarity, desolvation and electrostatics.
Proteins. Structure, Function and Genetics.  47: 281-294.

Haverty PM, Weng Z, Best N, Auerbach K, Hsiao L, Jensen RV, Gullans S. R. (2002) 
HugeIndex:  A Database with Visualization Tools for High Density Oligonucleotide Array Data from Normal Human Tissues. 
Nucleic Acids Research. 30:214-217. 

Weng Z, DeLisi C. (2002)
Protein Therapeutics: promises and challenges for the 21st century.
Trends in Biotechnology. 20:29-35.

Resendes BL, Robertson N, Szustakowski J, Resendes R, Weng Z, Morton C.  (2002) 
Gene discovery in the auditory system: characterization of additional cochlear expressed sequences. 
Journal of the Association for Research in Otolaryngology. 3:45-53. 

Hsiao LL, Dangond F, Yoshida T, Hong R, Jensen RV, Misra J, Dillon W, Lee KF, Clark KE, Haverty P, Weng Z, Mutter GL, Frosch MP, Macdonald ME, Milford EL, Crum CP, Bueno R, Pratt RE, Mahadevappa M, Warrington JA, Stephanopoulos G, Stephanopoulos G, Gullans SR. (2001) 
A compendium of gene expression in normal human tissues. 
Physiological Genomics. 7:97-104. 

Frith M, Hansen U, Weng Z. (2001) 
Detection of cis-element clusters in higher eukaryotic DNA. 
Bioinformatics.  17:878-889. 

Szustakowski J,  Weng Z. (2000) 
Protein Structure alignment using a genetic algorithm.  
Proteins. Structure, Function and Genetics.  38:428-440. 

Anderson A, Weng Z. (1999)  
VRDD: Applying virtual reality visualization to protein docking and design.  
J. Molecular Graphics & Modeling. 17:180-186. 

Esposito M, Venkatesh V, Otvos L, Weng Z, Vajda S, Banki K, Perl A. (1999) 
Human transaldolase and cross-reactive viral epitopes identified by autoantibodies of multiple sclerosis patients. 
J. Immunol. 163:4027-4032. 

Khanna R, Silins SL, Weng Z, Gatchell D, Burrows S, Cooper L. (1999) 
Cytotoxic T cell recognition of allelic variants of HLA B35 bound to an Epstein-Barr virus epitope: influence of peptide conformation and TCR-peptide interaction. 
Eur. J. Immunol. 29: 1587-1597. 

Skvorak AB, Weng Z, Yee AJ, Robertson NG, Morton CC. (1999) 
Human cochlear expressed sequence tags provide insight into cochlear gene expression and identify candidate genes for deafness. 
Hum. Molec. Genet. 8: 439-452. 

Camacho C, Weng Z, Vajda S, DeLisi C. (1999) 
Free Energy Landscapes of Encounter Complexes in Protein-Protein Association.  
BioPhys. J. 76: 1166-78. 

Weng Z, Gulukota K, Vaughn D, Bjorkman P, DeLisi C. (1998) 
Computational determination of the structure of Rat Fc bound to the neonatal Fc receptor. 
J. Mol. Biol. 282: 217-225. 

Weng Z, DeLisi C. (1998)
Toward a predictive understanding of molecular recognition.
Immuno. Rev. 163, 251-266. 

Zhang C, Kimura SR, Weng Z, Vajda S, Brower RC, DeLisi C. (1998) 
The waters of life. 
J. Franklin Inst. 335B, 213-240. 

DeLisi C, Cantor C, Weng Z. (1997) 
Hedgehogs, foxes, and a new science.
Nat. Biotechnol. 1997 Sep; 15(9):819

Weng Z, Delisi C, Vajda S. (1997) 
Empirical free energy calculation: comparison to calorimetric data. 
Protein Sci 6, 1976-84. 

Weng Z, Vajda S, Delisi C. (1996) 
Prediction of protein complexes using empirical free energy functions. 
Protein Sci 5, 614-26. 

Vajda S, Weng Z, DeLisi C. (1995) 
Extracting hydrophobicity parameters from solute partition and protein mutation/unfolding experiments. 
Protein Eng 8, 1081-92. 

Vajda S, Weng Z, Rosenfeld R, DeLisi C. (1994)
Effect of conformational flexibility and solvation on receptor-ligand binding free energies. 
Biochemistry 33, 13977-88.